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Guide to run {verdepcheck} strategies from a docker container

NEST CoreDev

Source: vignettes/run_with_docker_container.Rmd
run_with_docker_container.Rmd

verdepcheck can be used within a docker container to consistently check the version dependencies of an R package. This vignette demonstrates how to run the r-verdepcheck-action GitHub workflow locally with a minimal setup.

  1. Download the docker image
  2. Run the docker container
  3. Open RStudio in the browser
  4. Run the code below by changing the github_id to the repository you want to check

It assumes that you have docker installed on your machine.

Note: that you can skip the container setup and run the code below in your local R session.

Pull and run the docker image

The docker image used in this vignette is available on the GitHub Container Registry (ghcr.io) and is being used by the Insights Engineering R packages (such as teal and tern).

docker pull ghcr.io/insightsengineering/rstudio:latest
docker run --rm -p 8787:8787 -e PASSWORD=test -v ./:/workspace/project ghcr.io/insightsengineering/rstudio

Open the RStudio in the browser

Navigate to [http://localhost:8787] and login with the username rstudio and password test.

Clean pkgcache cache before repeated runs

In order to avoid using cached downloads from the previous run, it is recommend to clean the pkgcache directory.

# This command should be run inside the container
rm -rf /home/rstudio/.cache/R/pkgcache

note: The location of the pkgcache directory may vary depending on the operation system. Use the R command pkgcache::pkg_cache_summary() to find its location in your system.

Run the code below inside the container 

# Dependencies -----------------------------------------------------------------

renv::install(c("checkmate", "withr", "testthat"), prompt = FALSE)
renv::install("insightsengineering/verdepcheck", prompt = FALSE)

# Parameters -------------------------------------------------------------------

github_id <- "insightsengineering/teal.code"
ref <- NULL # --branch <name>, tag or NULL
depth <- "--depth 1" # --depth <depth number> or NULL
build_args <- " " # When empty it should have 1 space
r_cmd_check_args <- " " # When empty it should have 1 space
strategy <- "min_isolated" # one of min_isolated, min_cohort, release or max

# Logic to run action (don't change) -------------------------------------------

repo_path <- withr::local_tempfile(pattern = "repo")

checkmate::assert_string(github_id)
checkmate::assert_string(depth, null.ok = TRUE, pattern = "--depth [0-9]+")
checkmate::assert_string(ref, null.ok = TRUE, pattern = "--branch .+")
checkmate::assert_string(build_args)
checkmate::assert_string(r_cmd_check_args)
checkmate::assert_choice(strategy, c("min_isolated", "min_cohort", "release", "max"))

# Clone repository
system2(
  "git",
  args = list(
    "clone",
    depth,
    ref,
    paste0("https://github.com/", github_id),
    repo_path
  ) |> purrr::compact() # remove empty arguments if they are NULL
)

setwd(repo_path)

# Prepare arguments for script call
args <- c()
args[1] <- "" # path to file (should be empty for current directory)
args[2] <- build_args # build_args
args[3] <- r_cmd_check_args # check_args
args[4] <- strategy # strategy

# Mock the function inside the script
testthat::with_mocked_bindings(
  code = source("https://raw.githubusercontent.com/insightsengineering/r-verdepcheck-action/main/script.R"),
  commandArgs = function(...) args,
  .package = "base"
)